I don't think this is man-with-a-hammer syndrome, merely that the approach to building web apps translates well for 90% of native apps. For everything else, there's a FFI or NDK.
The major failing of ChromeOS, in my opinion, is that it needs an internet connection to work. (WebOS, for example, does not). The closest analog to "local" apps are browser extensions, and that is still a reasonable approach; the capabilities of such just need to be expanded a little. HTML5-style offline functionality is another option.
FWIW, most of my work is done in C these days. Different tools for different tasks.
Why limit to "Java"? For apps that aren't just front ends to web services, I'll take Cocoa, Android, or wxPython over HTML5.
Oh, please. http://en.wikipedia.org/wiki/Metonymy
And my point still stands. The majority of apps are either front ends to web services, or can be constructed using a similar approach that we use for the web today. They are UI-heavy. I did say you should be able to drop to native code if you really need the power.
Or the CPU running at its full potential rather than interpreting Javascript, or storage that doesn't have 100+ millisecond network latency, or UI frameworks that were designed for applications rather than text documents...
The web is great for lots of things. The insistence that it should be the One True Way for applications strikes me as a case of man-with-a-hammer syndrome.